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Catalina-Hernández È, López-Martín M, Masnou-Sánchez D, Martins M, Lorenz-Fonfria VA, Jiménez-Altayó F, Hellmich UA, Inada H, Alcaraz A, Furutani Y, Nonell-Canals A, Vázquez-Ibar JL, Domene C, Gaudet R, Perálvarez-Marín A. Experimental and computational biophysics to identify vasodilator drugs targeted at TRPV2 using agonists based on the probenecid scaffold. Comput Struct Biotechnol J 2024; 23:473-482. [PMID: 38261868 PMCID: PMC10796807 DOI: 10.1016/j.csbj.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/25/2024] Open
Abstract
TRP channels are important pharmacological targets in physiopathology. TRPV2 plays distinct roles in cardiac and neuromuscular function, immunity, and metabolism, and is associated with pathologies like muscular dystrophy and cancer. However, TRPV2 pharmacology is unspecific and scarce at best. Using in silico similarity-based chemoinformatics we obtained a set of 270 potential hits for TRPV2 categorized into families based on chemical nature and similarity. Docking the compounds on available rat TRPV2 structures allowed the clustering of drug families in specific ligand binding sites. Starting from a probenecid docking pose in the piperlongumine binding site and using a Gaussian accelerated molecular dynamics approach we have assigned a putative probenecid binding site. In parallel, we measured the EC50 of 7 probenecid derivatives on TRPV2 expressed in Pichia pastoris using a novel medium-throughput Ca2+ influx assay in yeast membranes together with an unbiased and unsupervised data analysis method. We found that 4-(piperidine-1-sulfonyl)-benzoic acid had a better EC50 than probenecid, which is one of the most specific TRPV2 agonists to date. Exploring the TRPV2-dependent anti-hypertensive potential in vivo, we found that 4-(piperidine-1-sulfonyl)-benzoic acid shows a sex-biased vasodilator effect producing larger vascular relaxations in female mice. Overall, this study expands the pharmacological toolbox for TRPV2, a widely expressed membrane protein and orphan drug target.
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Affiliation(s)
- Èric Catalina-Hernández
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Mario López-Martín
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - David Masnou-Sánchez
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Marco Martins
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Victor A. Lorenz-Fonfria
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán-2, 46980 Paterna, Spain
| | - Francesc Jiménez-Altayó
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Department of Pharmacology, Toxicology and Therapeutics,Institute of Neurosciences, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Ute A. Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry & Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Hitoshi Inada
- Department of Biochemistry & Cellular Biology National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8551, Japan
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Dept. of Physics, Universitat Jaume I, 12071 Castellón, Spain
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
- Optobiotechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
| | | | - Jose Luis Vázquez-Ibar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Carmen Domene
- Dept. of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Rachelle Gaudet
- Dept of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alex Perálvarez-Marín
- Unit of Biophysics, Dept. of Biochemistry and Molecular Biology, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
- Institute of Neurosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
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White O, Dehouck V, Boulanger N, Dierick F, Babič J, Goswami N, Buisseret F. Resonance tuning of rhythmic movements is disrupted at short time scales: A centrifuge study. iScience 2024; 27:109618. [PMID: 38650981 PMCID: PMC11033689 DOI: 10.1016/j.isci.2024.109618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
The human body exploits its neural mechanisms to optimize actions. Rhythmic movements are optimal when their frequency is close to the natural frequency of the system. In a pendulum, gravity modulates this spontaneous frequency. Participants unconsciously adjust their natural pace when cyclically moving the arm in altered gravity. However, the timescale of this adaptation is unexplored. Participants performed cyclic movements before, during, and after fast transitions between hypergravity levels (1g-3g and 3g-1g) induced by a human centrifuge. Movement periods were modulated with the average value of gravity during transitions. However, while participants increased movement pace on a cycle basis when gravity increased (1g-3g), they did not decrease pace when gravity decreased (3g-1g). We highlight asymmetric effects in the spontaneous adjustment of movement dynamics on short timescales, suggesting the involvement of cognitive factors, beyond standard dynamical models.
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Affiliation(s)
- Olivier White
- INSERM UMR1093-CAPS, Université de Bourgogne, UFR des Sciences du Sport, 21000 Dijon, France
| | - Victor Dehouck
- INSERM UMR1093-CAPS, Université de Bourgogne, UFR des Sciences du Sport, 21000 Dijon, France
| | - Nicolas Boulanger
- Service de Physique de l’Univers, Champs et Gravitation, UMONS Research Institute for Complex Systems, Université de Mons, 20 Place du Parc, 7000 Mons, Belgium
| | - Frédéric Dierick
- CeREF-Technique, Chaussée de Binche 159, 7000 Mons, Belgium
- Laboratoire d’Analyse du Mouvement et de la Posture (LAMP), Centre National de Rééducation Fonctionnelle et de Réadaptation—Rehazenter, Rue André Vésale 1, 2674 Luxembourg, Luxembourg
- Faculté des Sciences de la Motricité, UCLouvain, Place Pierre de Coubertin 2, 1348 Louvain-la-Neuve, Belgium
| | - Jan Babič
- Laboratory for Neuromechanics, and Biorobotics, Jožef Stefan Institute, Ljubljana, Slovenia
- Slovenia and also with the Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Nandu Goswami
- Gravitational Physiology and Medicine Research Unit, Otto Loewi Research Center of Vascular Biology, Immunity and Inflammation, Medical University of Graz, Graz, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Fabien Buisseret
- CeREF-Technique, Chaussée de Binche 159, 7000 Mons, Belgium
- Service de Physique Nucléaire et Subnucléaire, UMONS Research Institute for Complex Systems, Université de Mons, 20 Place du Parc, 7000 Mons, Belgium
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Wilke K, Nietzsche S, Hemmleb M, Mason S, Varghese R, Lang T, Gaengler P. Cervical wear pathobiology by robot-simulated 3-year toothbrushing - New methodological approach. Arch Oral Biol 2024; 163:105981. [PMID: 38669743 DOI: 10.1016/j.archoralbio.2024.105981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVES An ex-vivo study was aimed at (i) programming clinically validated robot three-year random toothbrushing, (ii) evaluating cervical macro- and microwear patterns on all tooth groups of different functional age, (iii) documenting and codificating wear related morphological features at the cemento-enamel junction in young teeth and on roots in older teeth. DESIGN Following ethical approval random toothbrushing (44 strokes per tooth horizontally, rotating, vertically; 2x/d) with manual toothbrushes and low-abrasive dentifrice was performed in an artificial oral cavity with brushing-force 3.5 N on 14 extracted human teeth. Morphological features were examined by SEM at baseline and after simulated 3 years using the replication technique. 3D-SEM analyses were carried out with a four-quadrant back scattered electron detector. Wilcoxon-Mann-Whitney-test was used for statistical analyses. RESULTS 3-year random toothbrushing with horizontal, rotating and vertical brushing movements revealed morphological features classified as four enamel patterns, one dentin pattern and three cervical patterns. Negative impacts were enamel, cementum and dentin loss. Positive impact on oral health was removing dental calculus and straightening cervical traumatic and iatrogenic damages. The volume loss varied from x̅=34.25nl to x̅=87.75nl. Wear extended apically from 100 to 1500 micrometres. CONCLUSION Robot simulated toothbrushing in an artificial oral cavity, with subsequent SEM and 3D-SEM assessment, elucidated both negative and oral health-contributing micromorphology patterns of cervical wear after simulated 3-year random toothbrushing. Cervical macro- and microwear of cementum revealed, for the first time, what we describe as overhanging enamel peninsulas and enamel islands on roots in young teeth, but no enamel islands on roots from older teeth after root cementum loss. In contrast, many older teeth exhibited enamel peninsulas.
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Affiliation(s)
- K Wilke
- ORMED - Institute for Oral Medicine at the University of Witten/Herdecke, Witten, Germany
| | - S Nietzsche
- Centre for Electron Microscopy, University Hospital Jena, Jena, Germany
| | - M Hemmleb
- Point electronic GmbH, Halle/Saale, Germany
| | - S Mason
- Haleon, Weybridge, Surrey, UK
| | | | - T Lang
- ORMED - Institute for Oral Medicine at the University of Witten/Herdecke, Witten, Germany
| | - P Gaengler
- ORMED - Institute for Oral Medicine at the University of Witten/Herdecke, Witten, Germany.
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Wang HY, Takagi H, Stoney PN, Echeverria A, Kuhn B, Hsu KS, Takahashi T. Anoxia-induced hippocampal LTP is regeneratively produced by glutamate and nitric oxide from the neuro-glial-endothelial axis. iScience 2024; 27:109515. [PMID: 38591010 PMCID: PMC11000013 DOI: 10.1016/j.isci.2024.109515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/17/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Transient anoxia causes amnesia and neuronal death. This is attributed to enhanced glutamate release and modeled as anoxia-induced long-term potentiation (aLTP). aLTP is mediated by glutamate receptors and nitric oxide (·NO) and occludes stimulation-induced LTP. We identified a signaling cascade downstream of ·NO leading to glutamate release and a glutamate-·NO loop regeneratively boosting aLTP. aLTP in entothelial ·NO synthase (eNOS)-knockout mice and blocking neuronal NOS (nNOS) activity suggested that both nNOS and eNOS contribute to aLTP. Immunostaining result showed that eNOS is predominantly expressed in vascular endothelia. Transient anoxia induced a long-lasting Ca2+ elevation in astrocytes that mirrored aLTP. Blocking astrocyte metabolism or depletion of the NMDA receptor ligand D-serine abolished eNOS-dependent aLTP, suggesting that astrocytic Ca2+ elevation stimulates D-serine release from endfeet to endothelia, thereby releasing ·NO synthesized by eNOS. Thus, the neuro-glial-endothelial axis is involved in long-term enhancement of glutamate release after transient anoxia.
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Affiliation(s)
- Han-Ying Wang
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
- Academia Sinica, Institute of Biomedical Sciences, Taipei 115, Taiwan
| | - Hiroshi Takagi
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
- Department of Neurosurgery, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Patrick N. Stoney
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Anai Echeverria
- Optical Neuroimaging Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Bernd Kuhn
- Optical Neuroimaging Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Kuei-Sen Hsu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Tomoyuki Takahashi
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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Jin X, Zhang Y, Wang D, Zhang X, Li Y, Wang D, Liang Y, Wang J, Zheng L, Song H, Zhu X, Liang J, Ma J, Gao J, Tong J, Shi L. Metabolite and protein shifts in mature erythrocyte under hypoxia. iScience 2024; 27:109315. [PMID: 38487547 PMCID: PMC10937114 DOI: 10.1016/j.isci.2024.109315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
As the only cell type responsible for oxygen delivery, erythrocytes play a crucial role in supplying oxygen to hypoxic tissues, ensuring their normal functions. Hypoxia commonly occurs under physiological or pathological conditions, and understanding how erythrocytes adapt to hypoxia is fundamental for exploring the mechanisms of hypoxic diseases. Additionally, investigating acute and chronic mountain sickness caused by plateaus, which are naturally hypoxic environments, will aid in the study of hypoxic diseases. In recent years, increasingly developed proteomics and metabolomics technologies have become powerful tools for studying mature enucleated erythrocytes, which has significantly contributed to clarifying how hypoxia affects erythrocytes. The aim of this article is to summarize the composition of the cytoskeleton and cytoplasmic proteins of hypoxia-altered erythrocytes and explore the impact of hypoxia on their essential functions. Furthermore, we discuss the role of microRNAs in the adaptation of erythrocytes to hypoxia, providing new perspectives on hypoxia-related diseases.
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Affiliation(s)
- Xu Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yingnan Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Ding Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xiaoru Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yue Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Di Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yipeng Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lingyue Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Haoze Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xu Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jing Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jinfa Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
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Müller M, Igamberdiev AU. The emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890-1938) in English translation. Biosystems 2024:105201. [PMID: 38642880 DOI: 10.1016/j.biosystems.2024.105201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/22/2024]
Abstract
Ervin Bauer (1890-1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of the living being on the basis of its thermodynamic properties and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920)Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935). These works became a bibliographical rarity. A complete English translation of "Theoretical Biology" is an important task for the future.
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Niknam Hamidabad M, Watson NA, Wright LN, Mansbach RA. In Silico Study of the Early Stages of Aggregation of β Sheet-forming Antimicrobial Peptide GL13K. Chembiochem 2024:e202400088. [PMID: 38572930 DOI: 10.1002/cbic.202400088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Antimicrobial peptides (AMPs) are of growing interest as potential candidates that may offer more resilience against antimicrobial resistance than traditional antibiotic agents. In this article, we perform the first in silico study of the synthetic ß sheet-forming AMP GL13K. Through atomistic simulations of single and multi-peptide systems under different conditions, we are able to shine a light on the short timescales of early aggregation. We find that isolated peptide conformations are primarily dictated by sequence rather than charge, whereas changing charge has a significant impact on the conformational free energy landscape of multi-peptide systems. We demonstrate that the loss of charge-charge repulsion is a sufficient minimal model for experimentally observed aggregation. Overall, our work explores the molecular biophysical underpinnings of the first stages of aggregation of a unique AMP, laying necessary groundwork for its further development as an antibiotic candidate.
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Affiliation(s)
| | - Natalya A Watson
- Concordia University, Physics, 7141 Sherbrooke St W, H4B 1R6, Montreal, CANADA
| | - Lindsay N Wright
- Concordia University, Physics, 7141 Sherbrooke St W, H4B 1R6, Montreal, CANADA
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8
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Ng PR, Bush A, Vissani M, McIntyre CC, Richardson RM. Biophysical Principles and Computational Modeling of Deep Brain Stimulation. Neuromodulation 2024; 27:422-439. [PMID: 37204360 DOI: 10.1016/j.neurom.2023.04.471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Deep brain stimulation (DBS) has revolutionized the treatment of neurological disorders, yet the mechanisms of DBS are still under investigation. Computational models are important in silico tools for elucidating these underlying principles and potentially for personalizing DBS therapy to individual patients. The basic principles underlying neurostimulation computational models, however, are not well known in the clinical neuromodulation community. OBJECTIVE In this study, we present a tutorial on the derivation of computational models of DBS and outline the biophysical contributions of electrodes, stimulation parameters, and tissue substrates to the effects of DBS. RESULTS Given that many aspects of DBS are difficult to characterize experimentally, computational models have played an important role in understanding how material, size, shape, and contact segmentation influence device biocompatibility, energy efficiency, the spatial spread of the electric field, and the specificity of neural activation. Neural activation is dictated by stimulation parameters including frequency, current vs voltage control, amplitude, pulse width, polarity configurations, and waveform. These parameters also affect the potential for tissue damage, energy efficiency, the spatial spread of the electric field, and the specificity of neural activation. Activation of the neural substrate also is influenced by the encapsulation layer surrounding the electrode, the conductivity of the surrounding tissue, and the size and orientation of white matter fibers. These properties modulate the effects of the electric field and determine the ultimate therapeutic response. CONCLUSION This article describes biophysical principles that are useful for understanding the mechanisms of neurostimulation.
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Affiliation(s)
| | - Alan Bush
- Harvard Medical School, Boston, MA, USA; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Matteo Vissani
- Harvard Medical School, Boston, MA, USA; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Cameron C McIntyre
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Robert Mark Richardson
- Harvard Medical School, Boston, MA, USA; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
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Dai T, Rich LJ, Seshadri M, Dasgupta S. Protocol to detect and quantify tumor hypoxia in mice using photoacoustic imaging. STAR Protoc 2024; 5:102993. [PMID: 38568814 PMCID: PMC10999710 DOI: 10.1016/j.xpro.2024.102993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/05/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Photoacoustic imaging (PAI) with co-registered ultrasound (US) is a hybrid non-invasive imaging modality that enables visualization and quantification of tumor hypoxia in live animals. Here, using a breast tumor xenograft model as an example, we present a stepwise protocol describing animal preparation, positioning, instrument setup, and US-PAI image acquisition procedures. This protocol also guides through detailed data analysis, explains functional readouts obtained from PAI, and discusses the potential application of the technology to study the hypoxic tumor microenvironment. For complete details on the use and execution of this protocol, please refer to Dai et al.1.
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Affiliation(s)
- Tao Dai
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Laurie J Rich
- FUJIFILM VisualSonics, Inc, Toronto, ON, Canada; Department of Oral Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Mukund Seshadri
- Department of Oral Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Subhamoy Dasgupta
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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10
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Hall D. Equations describing semi-confluent cell growth (I) Analytical approximations. Biophys Chem 2024; 307:107173. [PMID: 38241828 DOI: 10.1016/j.bpc.2024.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024]
Abstract
A set of differential equations with analytical solutions are presented that can quantitatively account for variable degrees of contact inhibition on cell growth in two- and three-dimensional cultures. The developed equations can be used for comparative purposes when assessing contribution of higher-order effects, such as culture geometry and nutrient depletion, on mean cell growth rate. These equations also offer experimentalists the opportunity to characterize cell culture experiments using a single reductive parameter.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164, Japan.
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11
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Gracia M, Lefèvre BM, Güell Alonso R, Cachoux V, Balakireva M, Guirao B, Cuvelier D, Bardin AJ, Bellaïche Y. Applying mechanical forces on Drosophila tissues in vivo using the StretchCo, a 3D-printable device. STAR Protoc 2024; 5:102851. [PMID: 38354083 PMCID: PMC10876908 DOI: 10.1016/j.xpro.2024.102851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Applying mechanical forces to tissues helps to understand morphogenesis and homeostasis. Additionally, recording the dynamics of living tissues under mechanical constraints is needed to explore tissue biomechanics. Here, we present a protocol to 3D-print a StretchCo device and use it to apply uniaxial mechanical stress on the Drosophila pupal dorsal thorax epithelium. We describe steps for 3D printing, polydimethylsiloxane (PDMS) strip cutting, and glue preparation. We detail procedures for PDMS strip mounting, tissue compaction, and live imaging upon force application. For additional details on the use and execution of this protocol, please refer to Cachoux et al. (2023)1 from which the StretchCo machine has been derived.
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Affiliation(s)
- Mélanie Gracia
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Polarity, Division and Morphogenesis lab, 75005 Paris, France
| | - Bénédicte M Lefèvre
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Stem Cells and Tissue Homeostasis lab, 75005 Paris, France
| | - Raquel Güell Alonso
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Stem Cells and Tissue Homeostasis lab, 75005 Paris, France
| | - Victoire Cachoux
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Polarity, Division and Morphogenesis lab, 75005 Paris, France
| | - Maria Balakireva
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Polarity, Division and Morphogenesis lab, 75005 Paris, France
| | - Boris Guirao
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Polarity, Division and Morphogenesis lab, 75005 Paris, France
| | - Damien Cuvelier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR144, Cell Biology and Cancer Department, System Biology of Cell Polarity and Cell Division lab, 75005 Paris, France
| | - Allison J Bardin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Stem Cells and Tissue Homeostasis lab, 75005 Paris, France.
| | - Yohanns Bellaïche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology Department, Polarity, Division and Morphogenesis lab, 75005 Paris, France.
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12
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Wijerathne T, Lacroix J. Voltage-clamp fluorometry to record flow-activated PIEZO1 currents and fluorometric signals. STAR Protoc 2024; 5:102789. [PMID: 38103195 PMCID: PMC10770629 DOI: 10.1016/j.xpro.2023.102789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/13/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
PIEZO channels sense mechanical forces through conformational rearrangements of a mechanosensory domain called blade. To probe these rearrangements in real time, we have inserted conformational-sensitive cyclic-permuted GFP into several positions of PIEZO1's blade. Here, we describe the step-by-step experimental procedure we developed to simultaneously measure flow-activated ionic currents and fluorometric signals in cells expressing these engineered constructs. We describe steps for performing transfection, seeding cells on coverslips, setting up a perfusion-based fluid shear application system, and performing voltage-clamp fluorometry. For complete details on the use and execution of this protocol, please refer to Ozkan et al. (2023).1.
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Affiliation(s)
- Tharaka Wijerathne
- Department of Basic Medical Sciences, Western University of Health Sciences, 309 East Second St., Pomona, CA 91766, USA
| | - Jerome Lacroix
- Department of Basic Medical Sciences, Western University of Health Sciences, 309 East Second St., Pomona, CA 91766, USA.
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13
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Liu D, Helmick HDB, Kokini JL, Bhunia AK. Protocol to reveal the binding partner of secreted housekeeping enzymes in Listeria monocytogenes via in silico prediction to in vivo validation. STAR Protoc 2024; 5:102839. [PMID: 38261516 PMCID: PMC10831104 DOI: 10.1016/j.xpro.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Numerous interacting protein partners exist without recognized interactive domains, necessitating a standardized methodology to decipher more in-depth interaction profiles. Here, we present a protocol to reveal the binding partner of a secreted housekeeping enzyme, alcohol acetaldehyde dehydrogenase (Listeria adhesion protein), in Listeria monocytogenes through in silico modeling and in vivo experiments. We describe steps for target protein modeling, biophysical profiling, ClusPro docking optimization, protein variant modeling, and docking comparison. We then provide detailed procedures for in vitro and in vivo protein binding validation. For complete details on the use and execution of this protocol, please refer to Liu et al.1.
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Affiliation(s)
- Dongqi Liu
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN 479067, USA; Purdue Institute of Inflammation, Immunology, and Infectious Disease, West Lafayette, IN 47907, USA.
| | | | - Jozef L Kokini
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Arun K Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN 479067, USA; Purdue Institute of Inflammation, Immunology, and Infectious Disease, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA.
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14
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Yildirim V, Sloot PMA. Protocol for analyzing emergence dynamics of diabetes with obesity using numerical continuation and bifurcation analysis. STAR Protoc 2024; 5:102880. [PMID: 38349789 PMCID: PMC10876977 DOI: 10.1016/j.xpro.2024.102880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/05/2024] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
Type 2 diabetes (T2D) is a multifactorial disease that slowly and inconspicuously progresses over years. Here, we present a protocol for analyzing slow progression dynamics of T2D with obesity. We describe steps for using software to exploit the differences between the timescales of the metabolic variables and using numerical continuation and bifurcation analysis. We detail procedures to analyze bi-stable system dynamics and identify the thresholds that separate healthy and diabetic states. For complete details on the use and execution of this protocol, please refer to Yildirim et al. (2023).1.
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Affiliation(s)
- Vehpi Yildirim
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, 1081 BT Amsterdam, the Netherlands; Institute for Advanced Study, University of Amsterdam, 1012 GC Amsterdam, the Netherlands.
| | - Peter M A Sloot
- Institute for Advanced Study, University of Amsterdam, 1012 GC Amsterdam, the Netherlands; Computational Science Lab, University of Amsterdam, 1098 XH Amsterdam, the Netherlands.
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15
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Singh SB, Rajput SS, Patil S, Subramanyam D. Protocol for measuring mechanical properties of live cells using atomic force microscopy. STAR Protoc 2024; 5:102870. [PMID: 38329878 PMCID: PMC10865473 DOI: 10.1016/j.xpro.2024.102870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Atomic force microscope (AFM) is a powerful and versatile tool to determine the physical properties of cells. The force-distance curves obtained from AFM experiments can be used to determine the stiffness and viscoelastic properties of cells. Here, we present a protocol for the determination of viscoelasticity from live cells such as Drosophila hemocytes or mouse embryonic stem cells using AFM. This protocol has potential application in determining the physical properties of cells in healthy and diseased conditions. For complete details on the use and execution of this protocol, please refer to Mote et al. (2020),1 and Singh et al. (2023).2.
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Affiliation(s)
- Surya Bansi Singh
- National Centre for Cell Science, SP Pune University Campus, Pune 411007, India; SP Pune University, Pune 411007, India
| | - Shatruhan Singh Rajput
- Indian Institute of Science Education and Research, Pune 411008, India; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Shivprasad Patil
- Indian Institute of Science Education and Research, Pune 411008, India.
| | - Deepa Subramanyam
- National Centre for Cell Science, SP Pune University Campus, Pune 411007, India.
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16
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Mulder EJ, Moser B, Delgado J, Steinhardt R, Esser-Kahn AP. Protocol for localized macrophage stimulation with small-molecule TLR agonist via fluidic force microscopy. STAR Protoc 2024; 5:102873. [PMID: 38427566 PMCID: PMC10918328 DOI: 10.1016/j.xpro.2024.102873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 03/03/2024] Open
Abstract
Here, we present a protocol to deliver nanoliter volumes of Toll-like receptor (TLR) agonist onto a culture of nuclear factor κB (NF-κB) reporter macrophages using fluidic force microscopy and a micron-scale probe. We describe steps for quantifying the dose of agonist by modeling their diffusion with experimental inputs. We then detail procedures for quantifying and categorizing macrophage responses to individual and varied doses and combining agonist concentration and macrophage response to analyze the NF-κB response to localized TLR stimulation. For complete details on the use and execution of this protocol, please refer to Mulder et al. (2024).1.
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Affiliation(s)
| | - Brittany Moser
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Jennifer Delgado
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Rachel Steinhardt
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Aaron P Esser-Kahn
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.
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17
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Wang R, Guo J, Yao H, Luo X, Deng Y, Tian Y, Zhang Y, Gao S. Protocol for near-infrared optogenetics manipulation of neurons and motor behavior in C. elegans using emissive upconversion nanoparticles. STAR Protoc 2024; 5:102858. [PMID: 38294907 PMCID: PMC10846378 DOI: 10.1016/j.xpro.2024.102858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/01/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
In deep tissue, optogenetics faces limitations with visible light. Here, we present a protocol for near-infrared (NIR) optogenetics manipulation of neurons and motor behavior in Caenorhabditis elegans using emissive upconversion nanoparticles (UCNPs). We describe steps for synthesizing and modifying UCNPs. We then detail procedures for regulating neurons using these UCNPs in the model organism C. elegans. Using NIR light allows for superior tissue penetration to manipulate neuronal activities and locomotion behavior. For complete details on the use and execution of this protocol, please refer to Guo et al.,1 Ao et al.,2 and Zhang et al.3.
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Affiliation(s)
- Ruipeng Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jingxuan Guo
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hanlu Yao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xuekai Luo
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yixiang Deng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuhang Tian
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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18
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Tingey M, Junod SL, Rush C, Yang W. Protocol for live-cell super-resolution imaging of transport of pre-ribosomal subunits through the nuclear pore complex. STAR Protoc 2024; 5:102790. [PMID: 38113144 PMCID: PMC10770744 DOI: 10.1016/j.xpro.2023.102790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Here, we present a protocol for single-molecule super-resolution imaging of the nuclear export of pre-ribosomal subunits pre-40S and pre-60S through nuclear pore complexes. We describe steps for plating cells and co-transfecting cells. We then detail steps for using single-point edge-excitation sub-diffraction microscopy, allowing visualization of real-time dynamics of the pre-ribosomal subunits. For complete details on the use and execution of this protocol, please refer to Junod et al. (2023).1.
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Affiliation(s)
- Mark Tingey
- Temple University Department of Biology, Philadelphia, PA 19122, USA.
| | - Samuel L Junod
- Temple University Department of Biology, Philadelphia, PA 19122, USA
| | - Coby Rush
- Temple University Department of Biology, Philadelphia, PA 19122, USA
| | - Weidong Yang
- Temple University Department of Biology, Philadelphia, PA 19122, USA.
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19
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Chae SJ, Kim DW, Igoshin OA, Lee S, Kim JK. Beyond microtubules: The cellular environment at the endoplasmic reticulum attracts proteins to the nucleus, enabling nuclear transport. iScience 2024; 27:109235. [PMID: 38439967 PMCID: PMC10909898 DOI: 10.1016/j.isci.2024.109235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
All proteins are translated in the cytoplasm, yet many, including transcription factors, play vital roles in the nucleus. While previous research has concentrated on molecular motors for the transport of these proteins to the nucleus, recent observations reveal perinuclear accumulation even in the absence of an energy source, hinting at alternative mechanisms. Here, we propose that structural properties of the cellular environment, specifically the endoplasmic reticulum (ER), can promote molecular transport to the perinucleus without requiring additional energy expenditure. Specifically, physical interaction between proteins and the ER impedes their diffusion and leads to their accumulation near the nucleus. This result explains why larger proteins, more frequently interacting with the ER membrane, tend to accumulate at the perinucleus. Interestingly, such diffusion in a heterogeneous environment follows Chapman's law rather than the popular Fick's law. Our findings suggest a novel protein transport mechanism arising solely from characteristics of the intracellular environment.
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Affiliation(s)
- Seok Joo Chae
- Department of Mathematical Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Dae Wook Kim
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Oleg A. Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Seunggyu Lee
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
- Division of Applied Mathematical Sciences, Korea University, Sejong 30019, Republic of Korea
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
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20
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Deni WH, Gao T, Wu J. Protocol for reconstituting peptides/peptidomimetics from DMSO to aqueous buffers for circular dichroism analyses. STAR Protoc 2024; 5:102850. [PMID: 38285735 PMCID: PMC10839526 DOI: 10.1016/j.xpro.2024.102850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/22/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
Circular dichroism (CD) spectrometry is a rapid technique for detecting protein secondary structure, particularly helicity. DMSO is used to ensure optimal solubility of peptides/peptidomimetics; however, its background absorbance hinders effective CD analysis. Here, we present a protocol for reconstituting peptides/peptidomimetics from DMSO to aqueous buffers for CD analyses. We describe steps for identifying chemicals that induce DMSO evaporation, extracting peptides/peptidomimetics from DMSO, and CD spectrometer setup and analysis. We then detail procedures for secondary structure analyses of reconstituted peptides/peptidomimetics. For complete details on the use and execution of this protocol, please refer to Gao et al. (2023).1.
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Affiliation(s)
- William H Deni
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Tong Gao
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jinhua Wu
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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21
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Durrieu L, Bush A, Colman-Lerner A. Protocol for FRAP-based estimation of nuclear import and export rates in single yeast cells. STAR Protoc 2024; 5:102876. [PMID: 38349788 PMCID: PMC10876970 DOI: 10.1016/j.xpro.2024.102876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Here, we present a protocol for estimating nuclear transport parameters in single cells. We describe steps for performing four consecutive fluorescence recovery after photobleaching experiments, fitting the obtained data to an ordinary differential equations model, and statistical analysis of the fittings using a specialized R package. This protocol permits the estimation of import and export rates, nuclear or cytosolic fixed fractions, and total number of molecules. For complete details on the use and execution of this protocol, please refer to Durrieu et al.1.
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Affiliation(s)
- Lucía Durrieu
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), Buenos Aires C1428EGA, Argentina.
| | - Alan Bush
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Alejandro Colman-Lerner
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), Buenos Aires C1428EGA, Argentina.
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22
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Evers TMJ, Babaei M, Mashaghi A. Probing human immune cell mechanics using acoustic force spectroscopy. STAR Protoc 2024; 5:102861. [PMID: 38367234 PMCID: PMC10879795 DOI: 10.1016/j.xpro.2024.102861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/19/2024] Open
Abstract
Immune cells continuously adapt their mechanical properties for proper circulation and elicitation of immune responses. Here, we provide a step-by-step protocol for probing the single-cell mechanical properties of primary human monocytes using acoustic force spectroscopy (AFS). We describe steps for the calibration of the AFS chips, the isolation of monocytes from buffy coats, and the probing of monocyte mechanics using AFS. We then detail the data analysis strategy. The protocol is useful for characterizing a wide range of immune cells under various conditions in physiology and pathology. For complete details on the use and execution of this protocol, please refer to Evers et al. 1 and Evers et al.2.
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Affiliation(s)
- Tom M J Evers
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands; Laboratory for Interdisciplinary Medical Innovations, Centre for Interdisciplinary Genome Research, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands.
| | - Mehrad Babaei
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands; Laboratory for Interdisciplinary Medical Innovations, Centre for Interdisciplinary Genome Research, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands; Laboratory for Interdisciplinary Medical Innovations, Centre for Interdisciplinary Genome Research, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands.
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23
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Yao Y, Liu Y, Liu X, Zhang X, Shi P, Zhang X, Zhang Q, Wei X. Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios. iScience 2024; 27:109074. [PMID: 38361618 PMCID: PMC10867447 DOI: 10.1016/j.isci.2024.109074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
DNA tweezers, with their elegant simplicity and flexibility, have been pivotal in biosensing and DNA computing. However, conventional tweezers are confined to a binary transformation pre/post target signal recognition, limiting them to presence/absence judgments. This study introduces bubble DNA tweezers (BDT), capable of three distinct conformations based on variable target signal ratios. In contrast to traditional compact tweezers, BDT features a looser structure centered around a non-complementary bubble domain located between the tweezer arms' connecting axis and target signal recognition jaws. This bubble triggers toehold-free DNA strand displacement, leading to three conformational changes at different target signal concentrations. BDT detects presence/absence and true concentration with remarkable specificity and sensitivity. This adaptability is not confined to ideal scenarios, proving valuable in complex, noisy environments. Our method facilitates target DNA/miRNA signal quantification within a specific length range, promising applications in clinical research and environmental detection, while inspiring future biological assay innovations.
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Affiliation(s)
- Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
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24
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Popović ME. Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla. ZOOLOGY 2024; 163:126158. [PMID: 38428123 DOI: 10.1016/j.zool.2024.126158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024]
Abstract
Bioenergetics and biothermodynamics are valuable tools in research on growth and metabolic processes of a wide range of organisms, including viruses, bacteria, fungi, algae and plants, as is shown by the many publications on this topic in the literature. These studies provide insight into growth and metabolism of individual species, as well as interactions between species, like the virus-host interaction (infection) and virus-virus interaction (competition). However, this approach has not yet been applied to animal species. The universality of biothermodynamics and bioenergetics provides a good motive to apply them in analysis of animals. In this research, we made a bioenergetic, biothermodynamic and kinetic characterization for the first time for an animal species - Anguilla anguilla L. (European eel). We made a comparative analysis on yellow (young adult) and silver (mature adult) phases. Metabolic processes were modeled as chemical reactions with characteristic thermodynamic properties: enthalpy, entropy and Gibbs energy. Moreover, Gibbs energy explained growth rates, through phenomenological equations. This analysis of animal metabolism and growth explained metabolic properties of yellow and silver A. anguilla, including the bioenergetic aspect of life history. Moreover, we compared thermodynamic properties of A. anguilla with those of its main macromolecular components and other organisms. The thermodynamic properties were explained by the structural properties of organisms. This research extends the bioenergetic and biothermodynamic approaches to zoology, which should allow analysis of the energetic aspect of animal metabolic processes, interactions with their environment and interactions with other organisms. Furthermore, it connects the macroscopic perspective of zoology with the microscopic perspectives of biochemistry, bioenergetics and biothermodynamics. This will provide a basis for development of mechanistic models of animal growth and metabolism.
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Affiliation(s)
- Marko E Popović
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Njegoševa 12, Belgrade 11000, Serbia.
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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Li Q, Calhoun VD, Pham TD, Iraji A. Exploring Nonlinear Dynamics In Brain Functionality Through Phase Portraits And Fuzzy Recurrence Plots. bioRxiv 2024:2023.07.06.547922. [PMID: 38405742 PMCID: PMC10888921 DOI: 10.1101/2023.07.06.547922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Much of the complexity and diversity found in nature are driven by nonlinear phenomena, and this holds true for the brain. Nonlinear dynamics theory has been successfully utilized in explaining brain functions from a biophysics standpoint, and the field of statistical physics continues to make substantial progress in understanding brain connectivity and function. This study delves into complex brain functional connectivity using biophysical nonlinear dynamics approaches. We aim to uncover hidden information in high-dimensional and nonlinear neural signals, with the hope of providing a useful tool for analyzing information transitions in functionally complex networks. By utilizing phase portraits and fuzzy recurrence plots, we investigated the latent information in the functional connectivity of complex brain networks. Our numerical experiments, which include synthetic linear dynamics neural time series and a biophysically realistic neural mass model, showed that phase portraits and fuzzy recurrence plots are highly sensitive to changes in neural dynamics, and they can also be used to predict functional connectivity based on structural connectivity. Furthermore, the results showed that phase trajectories of neuronal activity encode low-dimensional dynamics, and the geometric properties of the limit-cycle attractor formed by the phase portraits can be used to explain the neurodynamics. Additionally, our results showed that the phase portrait and fuzzy recurrence plots can be used as functional connectivity descriptors, and both metrics were able to capture and explain nonlinear dynamics behavior during specific cognitive tasks. In conclusion, our findings suggest that phase portraits and fuzzy recurrence plots could be highly effective as functional connectivity descriptors, providing valuable insights into nonlinear dynamics in the brain.
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Affiliation(s)
- Qiang Li
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, Georgia, USA
| | - Vince D Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, Georgia, USA
| | - Tuan D. Pham
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London E1 2AD, UK
| | - Armin Iraji
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, Georgia, USA
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Several transient binding events create a strong, adaptable interface between organelles. Nature 2024. [PMID: 38317004 DOI: 10.1038/d41586-023-04120-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
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28
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Paez‐Perez M, Kuimova MK. Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules. Angew Chem Int Ed Engl 2024; 63:e202311233. [PMID: 37856157 PMCID: PMC10952837 DOI: 10.1002/anie.202311233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.
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Affiliation(s)
- Miguel Paez‐Perez
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
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29
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Neutze R, Miller RJD. Energetic laser pulses alter outcomes of X-ray studies of proteins. Nature 2024; 626:720-722. [PMID: 38355996 DOI: 10.1038/d41586-024-00233-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
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30
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Dolgin E. Fresh tools for watching the 'lava lamps' of living cells. Nature 2024; 626:1152-1154. [PMID: 38413751 DOI: 10.1038/d41586-024-00547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
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31
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Akakpo L, Gasu EN, Mensah JO, Borquaye LS. Oplodiol and nitidine as potential inhibitors of Plasmodium falciparum dihydrofolate reductase: insights from a computational study. J Biomol Struct Dyn 2024; 42:1655-1669. [PMID: 37194452 DOI: 10.1080/07391102.2023.2212815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/05/2023] [Indexed: 05/18/2023]
Abstract
Many natural products have been shown to possess antiplasmodial activities, but their protein targets are unknown. This work employed molecular docking and molecular dynamics simulations to explore the inhibitory activity of some antiplasmodial natural products against wild-type and mutant strains of Plasmodium falciparum dihydrofolate reductase (PfDHFR). From the molecular docking study, 6 ligands preferentially bind at the active site of the DHFR domain with binding energies ranging from -6.4 to -9.5 kcal/mol. Interactions of compounds with MET55 and PHE58 were mostly observed in the molecular docking study. From the molecular dynamics study, the binding of 2 of the ligands-nitidine and oplodiol-was observed to be stable against all tested strains of PfDHFR. The average binding free energy of oplodiol in complex with the various PfDHFR strains was -93.701 kJ/mol whereas that of nitidine was -106.206 kJ/mol. The impressive in silico activities of the 2 compounds suggest they could be considered for development as potential antifolate agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loretta Akakpo
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Edward Ntim Gasu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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32
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Caballero-Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse-Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg CP. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nat Phys 2024; 20:310-321. [PMID: 38370025 PMCID: PMC10866705 DOI: 10.1038/s41567-023-02302-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/23/2023] [Indexed: 02/20/2024]
Abstract
Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole-a protuberance of the zygote's vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces.
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Affiliation(s)
| | - Rushikesh Shinde
- Laboratoire de Matière et Systèmes Complexes, Université de Paris Cité and CNRS, Paris, France
| | | | - Matilda Peruzzo
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Irene Steccari
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Vanessa Zheden
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jack Merrin
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Andrew Callan-Jones
- Laboratoire de Matière et Systèmes Complexes, Université de Paris Cité and CNRS, Paris, France
| | - Raphaël Voituriez
- Laboratoire Jean Perrin, Sorbonne Université and CNRS, Paris, France
- Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université and CNRS, Paris, France
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Li MCM, Cheng YK, Cui C, Chow SKH, Wong RMY, Kwok TC, Siu PM, Yang M, Tian M, Rubin C, Welch AA, Qin L, Law SW, Cheung WH. Biophysical and nutritional combination treatment for myosteatosis in patients with sarcopenia: a study protocol for single-blinded randomised controlled trial. BMJ Open 2024; 14:e074858. [PMID: 38176874 PMCID: PMC10773315 DOI: 10.1136/bmjopen-2023-074858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
INTRODUCTION Sarcopenia is characterised by age-related loss of skeletal muscle and function and is associated with risks of adverse outcomes. The prevalence of sarcopenia increases due to ageing population and effective interventions is in need. Previous studies showed that β-hydroxy β-methylbutyrate (HMB) supplement and vibration treatment (VT) enhanced muscle quality, while the coapplication of the two interventions had further improved muscle mass and function in sarcopenic mice model. This study aims to investigate the efficacy of this combination treatment in combating sarcopenia in older people. The findings of this study will demonstrate the effect of combination treatment as an alternative for managing sarcopenia. METHODS AND ANALYSIS In this single-blinded randomised controlled trial, subjects will be screened based on the Asian Working Group for Sarcopenia (AWGS) 2019 definition. 200 subjects who are aged 65 or above and identified sarcopenic according to the AWGS algorithm will be recruited. They will be randomised to one of the following four groups: (1) Control+ONS; (2) HMB+ONS; (3) VT+ONS and (4) HMB+VT + ONS, where ONS stands for oral nutritional supplement. ONS will be taken in the form of protein formular once/day; HMB supplements will be 3 g/day; VT (35 Hz, 0.3 g, where g=gravitational acceleration) will be received for 20 mins/day and at least 3 days/week. The primary outcome assessments are muscle strength and function. Subjects will be assessed at baseline, 3-month and 6-month post treatment. ETHICS AND DISSEMINATION This study was approved by Joint CUHK-NTEC (The Chinese University of Hong Kong and New Territories East Cluster) Clinical Research Management Office (Ref: CRE-2022.223-T) and conformed to the Declaration of Helsinki. Trial results will be published in peer-reviewed journals and disseminated at academic conferences. TRIAL REGISTRATION NUMBER NCT05525039.
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Affiliation(s)
- Meng Chen Michelle Li
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Yu Kin Cheng
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Can Cui
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Simon Kwoon Ho Chow
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
- Department of Orthopaedic Surgery, Stanford University, Stanford, California, USA
| | - Ronald Man Yeung Wong
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Timothy Cy Kwok
- Medicine and Therapeutics, The Chinese University of Hong Kong Faculty of Medicine, Hong Kong, Hong Kong
| | - Parco M Siu
- University of Hong Kong, Hong Kong, Hong Kong
| | - Minghui Yang
- Department of Orthopaedics and Traumatology, Beijing Jishuitan Hospital, Beijing, China
| | - Maoyi Tian
- Harbin Medical University, Harbin, China
- University of New South Wales, Sydney, New South Wales, Australia
| | - Clinton Rubin
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - A A Welch
- University of East Anglia, Norwich, UK
| | - Ling Qin
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Sheung Wai Law
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Wing Hoi Cheung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
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FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS Discov 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Kwon HC, Fairclough RH, Chen TY. Biophysical and Pharmacological Insights to CLC Chloride Channels. Handb Exp Pharmacol 2024; 283:1-34. [PMID: 35768555 DOI: 10.1007/164_2022_594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The CLC family encompasses two functional categories of transmembrane proteins: chloride conducting channels and proton-chloride antiporters. All members in this chloride channel/transporter family consist of two identical protein subunits, and each subunit forms an independent ion-transport pathway, a structural architecture known as "double barrel." These CLC proteins serve biological functions ranging from membrane excitability and cell volume regulation to acidification of endosomes. Despite their ubiquitous expression, physiological significance, and resolved molecular structures of some of the family members, the mechanisms governing these molecules' biophysical functions are still not completely settled. However, a series of functional and structural studies have brought insights into interesting questions related to these proteins. This chapter explores the functional peculiarities underlying CLC channels aided by information observed from the chloride-proton antiporters in the CLC family. The overall structural features of these CLC proteins will be presented, and the biophysical functions will be addressed. Finally, the mechanism of pharmacological agents that interact with CLC channels will also be discussed.
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Affiliation(s)
- Hwoi Chan Kwon
- Center for Neuroscience and Biophysics Graduate Group, University of California, Davis, CA, USA
| | - Robert H Fairclough
- Department of Neurology and the Biophysics Graduate Group, University of California, Davis, CA, USA
| | - Tsung-Yu Chen
- Center for Neuroscience, Department of Neurology, and Biophysics Graduate Group, University of California, Davis, CA, USA.
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Erba EB, Pastore A. The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions. Adv Exp Med Biol 2024; 3234:109-123. [PMID: 38507203 DOI: 10.1007/978-3-031-52193-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.
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Kramm K, Schröder T, Vera AM, Grabenhorst L, Tinnefeld P, Grohmann D. DNA Origami-Based Single-Molecule Force Spectroscopy and Applications. Methods Mol Biol 2024; 2694:479-507. [PMID: 37824019 DOI: 10.1007/978-1-0716-3377-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Over the last years, single-molecule force spectroscopy provided insights into the intricate connection between mechanical stimuli and biochemical signaling. The underlying molecular mechanisms were uncovered and explored using techniques such as atomic force microscopy and force spectroscopy using optical or magnetic tweezers. These experimental approaches are limited by thermal noise resulting from a physical connection of the studied biological system to the macroscopic world. To overcome this limitation, we recently introduced the DNA origami force clamp (FC) which is a freely diffusing nanodevice that generates piconewton forces on a DNA sequence of interest. Binding of a protein to the DNA under tension can be detected employing fluorescence resonance energy transfer (FRET) as a sensitive readout.This protocol introduces the reader to the working principles of the FC and provides instructions to design and generate a DNA origami FC customized for a protein of interest. Molecular cloning techniques are employed to modify, produce, and purify a custom DNA scaffold. A fluorescently labeled DNA suitable to detect protein binding via FRET is generated via enzymatic ligation of commercial DNA oligonucleotides. After thermal annealing of all components, the DNA origami FC is purified using agarose gel electrophoresis. The final section covers the interrogation of the FC using confocal single-molecule FRET measurements and subsequent data analysis to quantify the binding of a DNA-binding protein to its cognate recognition site under a range of forces. Using this approach, force-dependent DNA-protein interactions can be studied on the single-molecule level on thousands of molecules in a parallelized fashion.
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Affiliation(s)
- Kevin Kramm
- University of Regensburg, Department of Microbiology and Archaea Centre, Regensburg, Germany
| | - Tim Schröder
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Andrés Manuel Vera
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Lennart Grabenhorst
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Philip Tinnefeld
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for NanoScience (CeNS), Munich, Germany
| | - Dina Grohmann
- University of Regensburg, Department of Microbiology and Archaea Centre, Regensburg, Germany.
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Grasso N, Graziano R, Marzano S, D'Aria F, Merlino F, Grieco P, Randazzo A, Pagano B, Amato J. Unveiling the interaction between DNA G-quadruplexes and RG-rich peptides. Int J Biol Macromol 2023; 253:126749. [PMID: 37689293 DOI: 10.1016/j.ijbiomac.2023.126749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
G-quadruplexes are non-canonical DNA secondary structures formed within guanine-rich strands that play important roles in various biological processes, including gene regulation, telomere maintenance and DNA replication. The biological functions and formation of these DNA structures are strictly controlled by several proteins that bind and stabilize or resolve them. Many G-quadruplex-binding proteins feature an arginine and glycine-rich motif known as the RGG or RG-rich motif. Although this motif plays a crucial role in the recognition of such non-canonical structures, their interaction is still poorly understood. Here, we employed a combination of several biophysical techniques to provide valuable insights into the interaction between a peptide containing an RGG motif shared by numerous human G-quadruplex-binding proteins (NIQI) and various biologically relevant G-quadruplex DNA structures with different topologies. We also shed light on the key amino acids involved in the binding process. Our findings contribute to lay the basis for the development of a new class of peptide-based G-quadruplex ligands as an alternative to small molecules. These ligands may serve as valid tools for interfering in DNA-protein interactions, with potential therapeutic applications.
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Affiliation(s)
- Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Raffaele Graziano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
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39
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Baker N. Super-propulsion: how sharpshooting insects flick their pee. Nature 2023:10.1038/d41586-023-04167-z. [PMID: 38151550 DOI: 10.1038/d41586-023-04167-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
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40
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Williams C, Dong KC, Arkinson C, Martin A. Preparation of site-specifically fluorophore-labeled polyubiquitin chains for FRET studies of Cdc48 substrate processing. STAR Protoc 2023; 4:102659. [PMID: 37889757 PMCID: PMC10630674 DOI: 10.1016/j.xpro.2023.102659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
A critical step in the removal of polyubiquitinated proteins from macromolecular complexes and membranes for subsequent proteasomal degradation is the unfolding of an ubiquitin moiety by the cofactor Ufd1/Npl4 (UN) and its insertion into the Cdc48 ATPase for mechanical translocation. Here, we present a stepwise protocol for the assembly and purification of Lys48-linked ubiquitin chains that are fluorophore labeled at specific ubiquitin moieties and allow monitoring polyubiquitin engagement by the Cdc48-UN complex in a FRET-based assay. For complete details on the use and execution of this protocol, please refer to Williams et al. (2023).1.
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Affiliation(s)
- Cameron Williams
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Ken C Dong
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720
| | - Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720.
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41
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Barik D, Das S. Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches. STAR Protoc 2023; 4:102665. [PMID: 37889760 PMCID: PMC10751549 DOI: 10.1016/j.xpro.2023.102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/08/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
We have explored the design principles of noncanonical bistable switches using high-throughput bifurcation analysis of positive feedback loops under dual signaling. Here, we present a protocol to carry out bifurcation analysis using pseudo-potential energy of the dynamical system. We also describe steps to perform automated parameter searching for canonical and noncanonical switches and multi-parameter phase diagram analysis of these switches. For complete details on the use and execution of this protocol, please refer to Das et al.1.
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Affiliation(s)
- Debashis Barik
- School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, Telangana 500046, India.
| | - Soutrick Das
- School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, Telangana 500046, India
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42
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Buss DJ, Reznikov N, McKee MD. Attaching organic fibers to mineral: The case of the avian eggshell. iScience 2023; 26:108425. [PMID: 38034363 PMCID: PMC10687338 DOI: 10.1016/j.isci.2023.108425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/15/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023] Open
Abstract
Bird eggs possess a mineralized eggshell with a soft underlying fibrous membrane. These dissimilar material layers successfully evolved a structural attachment to each other as a conserved avian reproduction strategy essential to avian embryonic development, growth, and hatching of the chick. To understand how organic membrane fibers attach to shell mineral (calcite), 3D multiscale imaging including X-ray and electron tomography coupled with deep learning-based feature segmentation was used to show how membrane fibers are organized and anchored into shell mineral. Whole fibers embed into mineral across the microscale, while fine mineral projections (granules/spikes) insert into fiber surfaces at the nanoscale, all of which provides considerable surface area and multiscale anchorage at the organic-inorganic interface between the fibrous membrane and the shell. Such a reciprocal anchorage system occurring at two different length scales between organic fibers and inorganic mineral provides a secure attachment mechanism for avian eggshell integrity across two dissimilar materials.
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Affiliation(s)
- Daniel J. Buss
- Department of Anatomy and Cell Biology, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
| | - Natalie Reznikov
- Department of Anatomy and Cell Biology, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
| | - Marc D. McKee
- Department of Anatomy and Cell Biology, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
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43
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Fang R, Lu Y. Simulating the conformational dynamics of the ATPase complex on proteasome using its free-energy landscape. STAR Protoc 2023; 4:102182. [PMID: 37768828 PMCID: PMC10542641 DOI: 10.1016/j.xpro.2023.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/16/2023] [Accepted: 02/23/2023] [Indexed: 09/30/2023] Open
Abstract
The AAA+ ATPase complex on proteasome powers its functions through a series of intricate conformational transitions. Here, we describe a procedure to simulate the conformational dynamics of the proteasomal ATPase complex. We first empirically determined the free-energy landscape (FEL) of proteasome and then simulated proteasome's conformational changes as stochastic transitions on its FEL. We compared the FEL-predicted proteasomal behaviors with experimental measurements and analyzed the map of the ATPase's global dynamics to gain mechanistic insights into proteasomal degradation. For complete details on the use and execution of this protocol, please refer to Fang et al. (2022).1.
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Affiliation(s)
- Rui Fang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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44
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Maruyama T, Noda NN. Protocol for real-time imaging of membrane fission by mitofissin. STAR Protoc 2023; 4:102590. [PMID: 37738122 PMCID: PMC10520655 DOI: 10.1016/j.xpro.2023.102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/04/2023] [Accepted: 09/01/2023] [Indexed: 09/24/2023] Open
Abstract
Yeast mitofissin Atg44 is a mitochondrial intermembrane space protein that causes membrane fission required for mitophagy. Here, we present a protocol for observing Atg44-mediated membrane fission. We describe steps for recombinant Atg44 purification, lipid nanotube preparation as model membranes, and Atg44-mediated membrane fission real-time observation. We then detail procedures for tube radius estimation using confocal microscopy. This protocol can also be adapted to the study of membrane fission by other proteins. For complete details on the use and execution of this protocol, please refer to Fukuda et al. (2023).1.
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Affiliation(s)
- Tatsuro Maruyama
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan; Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan.
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45
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Schimmel L, Noordstra I. Epithelial cell spreading assay on E-cadherin-coated glass or PDMS substrates for microscopy-based analysis of cadherin adhesions. STAR Protoc 2023; 4:102626. [PMID: 37792537 PMCID: PMC10568414 DOI: 10.1016/j.xpro.2023.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Adherens junctions (AJs) are multi-protein adhesion structures that couple contractile actomyosin networks of epithelial cells within a tissue. Here, we present an epithelial cell spreading assay on E-cadherin-coated glass or polydimethylsiloxane (PDMS) substrates for detailed microscopy-based analysis of cadherin adhesions. We describe steps for preparation of glass coverslips and PDMS gels, E-cadherin coating, and epithelial cell spreading. Epithelial cells can be seeded on E-cadherin-coated surfaces, thereby mimicking AJ formation in X-Y dimension, making it suitable for microscopy analysis. For complete details on the use and execution of this protocol, please refer to Noordstra et al. (2023).1.
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Affiliation(s)
- Lilian Schimmel
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ivar Noordstra
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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46
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Shen H, Fu C, Zhang J, Feng B, Yu S. Protocol for determining protein dynamics using FT-IR spectroscopy. STAR Protoc 2023; 4:102587. [PMID: 38043057 PMCID: PMC10701451 DOI: 10.1016/j.xpro.2023.102587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/05/2023] [Accepted: 08/31/2023] [Indexed: 12/05/2023] Open
Abstract
In biological systems, protein function depends on spatial and temporal changes known as protein dynamics, which can be probed by amide hydrogen/deuterium (H/D) exchange. Here, we present a protocol for determining protein dynamics by Fourier-transform infrared (FT-IR) spectroscopy. We describe steps for protein sample preparation and FT-IR spectra collection. We then detail procedures for spectra analysis. Applications include the effects of protein mutation or protein and metal ion or ligand interactions on the protein H/D exchange rate. For complete details on the use and execution of this protocol, please refer to Yu et al. (2013).1.
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Affiliation(s)
- Hao Shen
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Cuiping Fu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Junting Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
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47
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Murugan NJ, Cariba S, Abeygunawardena S, Rouleau N, Payne SL. Biophysical control of plasticity and patterning in regeneration and cancer. Cell Mol Life Sci 2023; 81:9. [PMID: 38099951 PMCID: PMC10724343 DOI: 10.1007/s00018-023-05054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/12/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cells and tissues display a remarkable range of plasticity and tissue-patterning activities that are emergent of complex signaling dynamics within their microenvironments. These properties, which when operating normally guide embryogenesis and regeneration, become highly disordered in diseases such as cancer. While morphogens and other molecular factors help determine the shapes of tissues and their patterned cellular organization, the parallel contributions of biophysical control mechanisms must be considered to accurately predict and model important processes such as growth, maturation, injury, repair, and senescence. We now know that mechanical, optical, electric, and electromagnetic signals are integral to cellular plasticity and tissue patterning. Because biophysical modalities underly interactions between cells and their extracellular matrices, including cell cycle, metabolism, migration, and differentiation, their applications as tuning dials for regenerative and anti-cancer therapies are being rapidly exploited. Despite this, the importance of cellular communication through biophysical signaling remains disproportionately underrepresented in the literature. Here, we provide a review of biophysical signaling modalities and known mechanisms that initiate, modulate, or inhibit plasticity and tissue patterning in models of regeneration and cancer. We also discuss current approaches in biomedical engineering that harness biophysical control mechanisms to model, characterize, diagnose, and treat disease states.
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Affiliation(s)
- Nirosha J Murugan
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada.
- Allen Discovery Center, Tufts University, Medford, MA, USA.
| | - Solsa Cariba
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Nicolas Rouleau
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
- Allen Discovery Center, Tufts University, Medford, MA, USA
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Samantha L Payne
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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48
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Wu T, Hornsby M, Zhu L, Yu JC, Shokat KM, Gestwicki JE. Protocol for performing and optimizing differential scanning fluorimetry experiments. STAR Protoc 2023; 4:102688. [PMID: 37943662 PMCID: PMC10663957 DOI: 10.1016/j.xpro.2023.102688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is a widely used technique for determining the apparent melting temperature (Tma) of a purified protein. Here, we present a protocol for performing and optimizing DSF experiments. We describe steps for designing and performing the experiment, analyzing data, and optimization. We provide benchmarks for typical Tmas and ΔTmas, standard assay conditions, and upper and lower limits of commonly altered experimental variables. We also detail common pitfalls of DSF and ways to avoid, identify, and overcome them.
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Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Hornsby
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA
| | - Lawrence Zhu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua C Yu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA.
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49
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Xiang XW, Liu HT, Tao XN, Zeng YL, Liu J, Wang C, Yu SX, Zhao H, Liu YJ, Liu KF. Glioblastoma behavior study under different frequency electromagnetic field. iScience 2023; 26:108575. [PMID: 38125027 PMCID: PMC10730381 DOI: 10.1016/j.isci.2023.108575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 10/06/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The tumor-treating fields (TTFields) technology has revolutionized the management of recurrent and newly diagnosed glioblastoma (GBM) cases. To ameliorate this treatment modality for GBM and other oncological conditions, it is necessary to understand the biophysical principles of TTFields better. In this study, we further analyzed the mechanism of the electromagnetic exposure with varying frequencies and electric field strengths on cells in mitosis, specifically in telophase. In reference to previous studies, an intuitive finite element model of the mitotic cell was built for electromagnetic simulations, predicting a local increase in the cleavage furrow region, which may help explain TTFields' anti-proliferative effects. Cell experiments confirmed that the reduction in proliferation and migration of glioma cell by TTFields was in a frequency- and field-strength-dependent manner. This work provides unique insights into the selection of frequencies in the anti-proliferative effect of TTFields on tumors, which could improve the application of TTFields.
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Affiliation(s)
- Xiao-Wei Xiang
- Academy for engineering & technology, Fudan University, Shanghai 200433, China
| | - Hao-Tian Liu
- Academy for engineering & technology, Fudan University, Shanghai 200433, China
| | - Xiao-Nan Tao
- School of information science and technology, Fudan University, Shanghai 200433, China
| | - Yu-Lian Zeng
- Department of Anesthesiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Jing Liu
- School of information science and technology, Fudan University, Shanghai 200433, China
| | - Chen Wang
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Sai-Xi Yu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hui Zhao
- School of information science and technology, Fudan University, Shanghai 200433, China
| | - Yan-Jun Liu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ke-Fu Liu
- School of information science and technology, Fudan University, Shanghai 200433, China
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50
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Hayashi K, Sasaki K. Number of kinesins engaged in axonal cargo transport: A novel biomarker for neurological disorders. Neurosci Res 2023; 197:25-30. [PMID: 37734449 DOI: 10.1016/j.neures.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Kinesin motor proteins play crucial roles in anterograde transport of cargo vesicles in neurons, moving them along axons from the cell body towards the synaptic region. Not only the transport force and velocity of single motor protein, but also the number of kinesin molecules involved in transporting a specific cargo, is pivotal for synapse formation. This collective transport by multiple kinesins ensures stable and efficient cargo transport in neurons. Abnormal increases or decreases in the number of engaged kinesin molecules per cargo could potentially act as biomarkers for neurodegenerative diseases such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis (ALS), spastic paraplegia, polydactyly syndrome, and virus transport disorders. We review here a model constructed using physical measurements to quantify the number of kinesin molecules associated with their cargo, which could shed light on the molecular mechanisms of neurodegenerative diseases related to axonal transport.
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Affiliation(s)
- Kumiko Hayashi
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.
| | - Kazuo Sasaki
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan
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